List of all items

Structs

• AtomDynamics
• BarostatCfg
• Dihedral
• ForcesOnWaterMol
• MdConfig
• MdOverrides
• MdState
• MolDynamics
• ParamError
• ShrinkingBoxCfg
• ShrinkingBoxPackingCfg
• SimBox
• WaterInitTemplate
• WaterMolOpc
• alchemical::DecouplingSchedule
• alchemical::LambdaWindow
• alchemical::StateAlchemical
• alchemical::TiEstimate
• param_inference::AmberDefSet
• param_inference::AtomEnvData
• params::FfParamSet
• params::ParamGeneralPaths
• params::ProtFfChargeMapSet
• snapshot::HydrogenBond
• snapshot::Snapshot
• snapshot::SnapshotEnergyData
• snapshot::SnapshotHandlers

Enums

• ComMotionRemoval
• ComputationDevice
• CustomSolventCount
• FfMolType
• HydrogenConstraint
• SimBoxInit
• Solvent
• SolventTemplateType
• alchemical::AlchemicalError
• integrate::Integrator
• snapshot::HBondAtomType

Functions

• alchemical::collect_window
• alchemical::free_energy_ti
• alchemical::free_energy_ti_with_sem
• alchemical::mean_coupled_interaction_kcal
• alchemical::staged_decoupling_schedule
• compute_energy_snapshot
• find_planar_posit
• find_tetra_posit_final
• find_tetra_posits
• make_octanol
• make_water_mols_grid
• merge_params
• pack_solvent_with_shrinking_box
• pack_solvent_with_shrinking_box_cfg
• param_inference::assign_missing_params
• param_inference::find_ff_types
• param_inference::matches_def
• param_inference::update_small_mol_params
• params::populate_peptide_ff_and_q
• params::prepare_peptide
• params::prepare_peptide_mmcif
• partial_charge_inference::infer_charge
• populate_hydrogens_dihedrals
• snapshot::gromacs_frames_to_ss
• snapshot::ss_to_gromacs_frames
• water_mols_from_template
• water_mols_from_template_in_region

Type Aliases

• params::LipidFfChargeMap
• params::NucleicAcidFfChargeMap
• params::ProtFfChargeMap

Constants

• LANGEVIN_GAMMA_DEFAULT
• LINCS_ITER_DEFAULT
• LINCS_ORDER_DEFAULT
• OCTANOL_WATER_TEMPLATE
• PRESSURE_DEFAULT
• SHAKE_TOL_DEFAULT
• TAU_PRESSURE_DEFAULT
• TAU_TEMP_DEFAULT
• WATER_TEMPLATE_60A
• alchemical::SOFT_CORE_ALPHA
• alchemical::SOFT_CORE_POWER
• alchemical::SOFT_CORE_SIGMA_MIN
• params::AMINO_19
• params::LIPID_21_LIB
• params::OL24_LIB
• params::RNA_LIB